Sindhikara, Daniel J.; Emerson, Daniel J.; Roitberg, Adrian E.. Exchange Often and Properly in Replica Exchange Molecular Dynamics. Journal of Chemical Theory and Computation., 2010-07-28 Abstract: Previous work by us showed that in replica exchange molecular dynamics, exchanges should be… Read More

Fernandez-Alberti, S.; Kleiman, Valeria D.; Tretiak, S.; Roitberg, Adrian E.. Unidirectional Energy Transfer in Conjugated Molecules: The Crucial Role of High-Frequency C-C Bonds. Journal of Physical Chemistry Letters., 2010-09-02 Abstract: Excited-state nonadiabatic molecular dynamics is used to study energy transfer… Read More

Swails, Jason M.; Meng, Yilin; Walker, F. Ann; Marti, Marcelo A.; Estrin, Dario A.; Roitberg, Adrian E.. pH-Dependent Mechanism of Nitric Oxide Release in Nitrophorins 2 and 4. Journal of Physical Chemistry B., 2009-01-22 Abstract: Nitrophorins are NO carrier proteins… Read More

Fernandez-Alberti, Sebastian; Kleiman, Valeria D.; Tretiak, Sergei; Roitberg, Adrian E.. Nonadiabatic Molecular Dynamics Simulations of the Energy Transfer between Building Blocks in a Phenylene Ethynylene Dendrimer. Physical Chemistry A., 2009-04-20 Abstract: The ultrafast dynamics of electronic and vibrational energy transfer… Read More

Dolghih, Elena; Ortiz, Wilfredo; Kim, Seonah; Krueger, Brent P.; Krause, Jeffrey L.; Roitberg, Adrian E.. Theoretical Studies of Short Polyproline Systems: Recalibration of a Molecular Ruler Journal of Physical Chemistry A., 2009-03-05 Abstract: FRET experiments enable studies of the chemical… Read More

Seabra, Gustavo de M.; Walker, Ross C.; Roitberg, Adrian E.. Are Current Semiempirical Methods Better Than Force Fields? A Study from the Thermodynamics Perspective Journal of Physical Chemistry A., 2009-07-15 Abstract: The semiempirical Hamiltonians MNDO, AM1, PM3, RM1, PDDG/MNDO, PDDG/PM3,… Read More

Demir, Oezlem; Roitberg, Adrian E.. Modulation of Catalytic Function by Differential Plasticity of the Active Site: Case Study of Trypanosoma cruzi trans-Sialidase and Trypanosoma rangeli Sialidase. Biochemistry, 2009-03-05 Abstract: FRET experiments enable studies of the chemical and physical properties of… Read More

Sindhikara, Daniel J.; Kim, Seonah; Voter, Arthur F.; Roitberg, Adrian E.. Bad Seeds Sprout Perilous Dynamics: Stochastic Thermostat Induced Trajectory Synchronization in Biomolecules Journal of Chemical Theory and Computation, 2009-04-28 Abstract: Molecular dynamics simulations starting from different initial conditions are… Read More

Mayoral, Jaime G.; Nouzova, Marcela; Yoshiyama, Micho; Shinod, Tetsuro; HernandezMartinez, Salvador; Dolghih, Elena; Turjanski, Adrian G.; Roitberg, Adrian E.; Priestap, Horacio; Perez, Mario; Mackenzie, Lucy; Li, Yiping; Noriega, Fernando G.. Molecular and functional characterization of a juvenile hormone acid methyltransferase… Read More

Torras, Juan; Seabra, Gustavo; Roitberg, Adrian E.. A Multiscale Treatment of Angeli’s Salt Decomposition Journal of Chemical Theory and Computation, 2008-12-12 Abstract: Sodium trioxodinitrate’s (Na2N2O3, Angeli’s salt) unique cardiovascular effects have been associated with its ability to yield HNO upon… Read More